Options Structure

Overview

The RunPreproc function takes two arguments: paths, a cell array that specifies the input image filenames, and opt, a structure that specifies the options. The fields of the opt structure are detailed here. The subfields of do are all false by default.

Set-up options

Option	Type	Description	Notes
opt.dir_out	string	Output directory	Default: 'output'. Files in ‘path’ are copied to the output directory. Files ending ‘.gz’ are gunzipped (in which case outputs will be gzipped). Regular images are written int16. If label images are specified, these are checked so that values are <= 255 and written uint8.
opt.prefix	string	Filename prefix	Default: 'pp_'. Added to filenames during initial copy.
opt.labels.part	multi	Values to use to collapse labels.	First, rounds label image values. Next, if part is a string, binarises label values to zero and nonzero. If part is a vector, assigns sequential values to voxels with each value in the vector. If part is a cell array, assigns sequential labels to voxels with any of the values in each cell.

Erode

Option	Type	Description	Notes
opt.do.erode	Boolean	Enable erode step	Removes a few of the outer voxels

Reset origin

Option	Type	Description	Notes
opt.do.res_orig	Boolean	Enable resetting origin	Important for CT
opt.reset_orig.only_neg	Boolean	Only reset origin if image contains negative values.	Negative values mean the image might be a CT.

Realignment to MNI space

Option	Type	Description	Notes
opt.do.real_mni	Boolean	Enable realignment
opt.realign2mni.rigid	Boolean	Make realignment rigid	Default: true.

Reslice to world space

Option	Type	Description	Notes
opt.do.nm_reorient	Boolean	Enable reslicing	The orientation matrix is applied to the image and reset.

Crop

Option	Type	Description	Notes
opt.do.crop	Boolean	Enable cropping	Remove unneccesary data to reduce image size
opt.crop.keep_neck	Boolean	Keep neck when cropping	Default: true. False makes for even smaller image

Coregistration

Option	Type	Description	Notes
opt.do.coreg	Boolean	Enable coregistration	Uses Normalised Mutual Information (NMI)
opt.coreg.ref	integer	Reference image	Default: 1. Which of the images acts as target for the others? Specify index in cell array paths{1}.

Denoising

Option	Type	Description	Notes
opt.do.denoise	Boolean	Enable denoising

Super-resolution

Option	Type	Description	Notes
opt.do.superres	Boolean	Enable super-resolution
opt.superres.ix	integer vector (N img)	Index of images to super-resolve	Vector the same length as cell array of images. Number indicates channel (i.e. modality). Examples: [1 1 1] specifies three observations of one channel. [1 1 2 2 3 3] specifies two observations each of three channels. Default = [], which is interpreted as one observation from each channel.
opt.superres.verbose	Boolean	Enable verbose output from super-resolution	Default: false.

Reslice images

Option	Type	Description	Notes
opt.do.reslice	Boolean	Reslice images to have same image grids	Only done if super-resolution is disabled.
opt.reslice.ref	string	Reference image	Default: 1. Which of the images acts as target for the others? Specify index in cell array paths{1} if labels specified.
opt.reslice.deg	integer	Interpolation order	Default: 1. 0 = nearest neighbour. 1 = trilinear. >=2 gives degree of B-spline.

Resize voxels

Option	Type	Description	Notes
opt.do.vx	Boolean	Change voxel size	If super-resolution is disabled, change voxel size when resetting origin, applying bounding box, or in a separate step (see detailed pipeline).
opt.vx.size	number	Specify voxel size in mm.	Default: 1.
opt.vx.deg	integer	Interpolation order	Default: 1. 0 = nearest neighbour. 1 = trilinear. >=2 gives degree of B-spline.

Apply SPM12 bounding box

Option	Type	Description	Notes
opt.do.bb_spm	Boolean	Make image have same bounding-box as default SPM12 template	Requires realignment to MNI.
opt.bb.dim	[integer,integer,integer]	Output dimensions after applying bounding-box	By default the atlas dimensions will be used

Unified segmentation

Option	Type	Description	Notes
opt.do.segment	Boolean	Enable unified segmentation
opt.segment.write_tc	Boolean matrix (6x4)	Select tissue classes to write	Default native space GM, WM and CSF. Rows: tissue classes. Columns: image to write (native space, DARTEL import, standard space unmodulated, standard space modulated).
opt.segment.write_bf	Boolean	Write bias correction results	Default: false. Can be a scalar, column vector length 2, or matrix N images x 2. Columns: write bias corrected image, write bias field.
opt.segment.write_df	Boolean	Write deformation fields	Default: false. Can be scalar or column vector length 2. 1: write forward. 2: write inverse.
opt.segment.dir_out	string	Directory to save segmentation output
opt.segment.make_4d	Boolean	Write 4D nifti with segmentations.
opt.segment.domask	Boolean	Enable cost function masking	Typically, a lesion mask is used to exclude abnormal voxels from segmentation.
opt.segment.maskvol	integer	Mask volume	Specify index in cell array paths.

Bias field correction

Option	Type	Description	Notes
opt.do.bfcorr	Boolean	Enable bias field correction	Depends on segmentation

Skull stripping

Option	Type	Description	Notes
opt.do.skullstrip	Boolean	Skull strip	Depends on segmentation

Align output to template

Option	Type	Description	Notes
opt.pth_template	string	Path to template	Used to reslice and affinely register images to a template.

Write images warped to MNI space

Option	Type	Description	Notes
opt.do.normalise	Boolean	Enable writing normalised images
opt.normalise.vox	integer or column vector (3)	Specify voxel size	If integer, outputs cubic voxels this size. If row vector uses these dimensions. Default from SPM (usually [2 2 2]).
opt.normalise.deg	integer	Interpolation order	Default: spm_get_defaults('normalise.write.interp'). 0 = nearest neighbour. 1 = trilinear. >=2 gives degree of B-spline.

Intensity normalisation

Option	Type	Description	Notes
opt.do.int_norm	Boolean	Enable intensity normalisation
opt.int_norm.rng	vector (2)	Range into which to normalise intensities	Default: [0 1]

Write 2D images

Option	Type	Description	Notes
opt.do.write2d	Boolean	Write 2D versions	If segmentation was run, writes 2D versions of segmented images too.
opt.dir_out2d	string	Directory to save 2D versions
opt.write2d.deg	integer	Interpolation order	Default: 0. 0 = nearest neighbour. 1 = trilinear. >=2 gives degree of B-spline.
opt.write2d.sliceix	integer	Slice index	This slice is written to the 2D file for each axis.

Output options

Option	Type	Description	Notes
opt.do.go2native	Boolean	Write images in native space
opt.do.writemat	Boolean	Save orientation matrix to .mat file